[R-sig-hpc] Error in UseMethod("stopCluster") : no applicable method for 'stopCluster' ...

[Marius Hofert]

Dear Martin,

Thanks for your help. I tried to put in library(parallel) in your example (see
below), but I still obtain

,----
| Error in NextMethod() : 'NextMethod' called from an anonymous function
`----

Do you know why?

Cheers,

Marius

grid <- expand.grid(a=1:4, b=2:10)
ngrid <- nrow(grid)
f <- function(x) sum(x)

library(parallel)

ex <- function() {
    cl <- makeCluster(detectCores(), type="MPI")
    stopCluster(cl)
}

res <- ex()



Martin Morgan <mtmorgan at fhcrc.org> writes:

> On 9/21/2012 12:16 PM, Marius Hofert wrote:
>> Dear Martin,
>>
>> thanks for helping. Is there a solution without explicitly loading snow/parallel
>> with library()/require()? I forgot to say, I was hoping for such a solution.
>
> Not that I know of. Write a package and importFrom(parallel, stopCluster)?
> Martin
>
>>
>> Cheers,
>>
>> Marius
>>
>> Martin Morgan <mtmorgan at fhcrc.org> writes:
>>
>>> On 09/21/2012 12:47 AM, Marius Hofert wrote:
>>>> Dear expeRts,
>>>>
>>>> If I run the minimal example below, I obtain:
>>>>
>>>> Loading required package: Rmpi
>>>> Loading required package: grDevices
>>>> Loading required package: grDevices
>>>> Loading required package: grDevices
>>>> Loading required package: grDevices
>>>> 	4 slaves are spawned successfully. 0 failed.
>>>> Error in UseMethod("stopCluster") :
>>>>     no applicable method for 'stopCluster' applied to an object of class "c('spawnedMPIcluster', 'MPIcluster', 'cluster')"
>>>>
>>>> However, if I run the body of the function (linewise; without calling the
>>>> function), everything works. Why is that so?
>>>>
>>>> Cheers,
>>>>
>>>> Marius
>>>>
>>>>
>>>> grid <- expand.grid(a=1:4, b=2:10)
>>>> ngrid <- nrow(grid)
>>>> f <- function(x) sum(x)
>>>>
>>>> ex <- function() {
>>>>       cl <- snow::makeCluster(parallel::detectCores(), type="MPI")
>>>>       on.exit(snow::stopCluster(cl))
>>>>       RNGkind("L'Ecuyer-CMRG")
>>>>       parallel::clusterExport(cl, varlist=c("f", "grid"))
>>>>       parallel::clusterApply(cl, seq_len(ngrid), function(i) f(grid[i,]))
>>>> }
>>>>
>>>> res <- ex()
>>>
>>> An even more minimal example is
>>>
>>>    ex <- function() {
>>>        cl <- snow::makeCluster(parallel::detectCores(), type="MPI")
>>>        snow::stopCluster(cl)
>>>    }
>>>    res <- ex()
>>>
>>> To be clear, there is no library(snow) in the script, and on.exit() is not
>>> relevant. The reason is that snow::stopCluster is an S3 generic, and on the help
>>> page ?NextMethod we have
>>>
>>>
>>>       Namespaces can register methods for generic functions.  To support
>>>       this, 'UseMethod' and 'NextMethod' search for methods in two
>>>       places: first in the environment in which the generic function is
>>>       called, and then in the registration data base for the environment
>>>       in which the generic is defined (typically a namespace).  So
>>>       methods for a generic function need to be available in the
>>>       environment of the call to the generic, or they must be
>>>       registered.  (It does not matter whether they are visible in the
>>>       environment in which the generic is defined.)
>>>
>>> There are no stopCluster methods defined in the calling namespace (i.e., your
>>> script) and since there has been no call to library(snow), there is no snow
>>> namespace to search and hence no method to be found.
>>>
>>> The solution is to add
>>>
>>>    library(snow)
>>>
>>> to the script (or better library(parallel) and use the 'parallel' library
>>> throughout).
>>>
>>> Martin
>>>
>>>
>>>>
>>>> _______________________________________________
>>>> R-sig-hpc mailing list
>>>> R-sig-hpc at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>>>
>>

--
ETH Zurich
Dr. Marius Hofert
RiskLab, Department of Mathematics
HG E 65.2
Rämistrasse 101
8092 Zurich
Switzerland

Phone +41 44 632 2423
http://www.math.ethz.ch/~hofertj